Within Switzerland, you only need the motorway vignette: myswissalps.com/ motorwayvignette. There are no other tolls or taxes. Within France you probably need to pay toll a couple of times, but I don't know details about that.

It is not easy to avoid the motorways. The tax ( vignette, carnet) costs about 40 CHF. (See the link Arno mentioned.) If you are driving any distance, the motorways make the trip a lot easier and faster. Time is money when you are on vacation. At least it is for me. ;-)

How will you cross the border without using the motorways? Do you know the back roads and border crossings well?